LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 8 of total 8

Search options

  1. Article ; Online: Conformational perturbation of peptides in presence of polar organic solvents.

    Yadav, Neetu Singh / Choudhury, Devapriya

    Journal of molecular graphics & modelling

    2019  Volume 89, Page(s) 1–12

    Abstract: The critical role played by solvent environment in maintaining the conformational integrity of peptides and proteins is accepted without question. Numerous experiments have suggested that perturbing the solvent environment of peptides and proteins by the ...

    Abstract The critical role played by solvent environment in maintaining the conformational integrity of peptides and proteins is accepted without question. Numerous experiments have suggested that perturbing the solvent environment of peptides and proteins by the addition of polar organic solvents have important consequences for the conformation of these molecules. However, experimental studies of such perturbations often report different kinds of effects depending on the solvent used and/or the sequence/structure of the molecule under study. In this work we report a simulation based comparative study on the effects of adding two common organic solvents viz. Dimethyl sulfoxide (DMSO) and Acetonitrile (MeCN) on the dynamical conformation of a test peptide Ace-Gly-X-Gly-Nme where X is any amino acid. Our studies identify important differences in peptide solvation by these two solvents, which we attempt to correlate with the kinetic stability of the conformation, as well as the identity of the central 'X' residue in the test peptide.
    MeSH term(s) Algorithms ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Chemical ; Models, Molecular ; Molecular Dynamics Simulation ; Organic Chemicals/chemistry ; Peptides/chemistry ; Protein Conformation ; Solvents/chemistry
    Chemical Substances Organic Chemicals ; Peptides ; Solvents
    Language English
    Publishing date 2019-02-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1396450-1
    ISSN 1873-4243 ; 1093-3263
    ISSN (online) 1873-4243
    ISSN 1093-3263
    DOI 10.1016/j.jmgm.2019.02.009
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 3491: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  2. Article: A statistical geometry analysis of simulated water-DMSO and water-MeCN binary mixtures for biomolecular studies.

    Yadav, Neetu Singh / Choudhury, Devapriya

    Bioinformation

    2018  Volume 14, Issue 7, Page(s) 350–356

    Abstract: Water-Dimethylsulfoxide (DMSO) and water-Acetonitrile (MeCN) binary mixtures at various molar ratios ranging from 0 to 1 are studied using Molecular Dynamics (MD) simulations. Hydration properties of water in different regions of MeCN/DMSO are ... ...

    Abstract Water-Dimethylsulfoxide (DMSO) and water-Acetonitrile (MeCN) binary mixtures at various molar ratios ranging from 0 to 1 are studied using Molecular Dynamics (MD) simulations. Hydration properties of water in different regions of MeCN/DMSO are investigated by using the statistical geometry approach. The obtained results reveal that in water-DMSO simulations both water and solvent molecules prefer to be in mixed cluster forms, depending upon the concentration of DMSO. While in case of water-MeCN mixtures, self-association of water and acetonitrile molecules, take place, showing microheterogeneity associated with the water- MeCN binary mixtures. The results highlight the utility of statistical geometric analysis of MD simulation data of binary liquid mixtures for rapid screening of polar organic solvents in non-aqueous enzymology.
    Language English
    Publishing date 2018-07-31
    Publishing country Singapore
    Document type Journal Article
    ZDB-ID 2203786-X
    ISSN 0973-2063
    ISSN 0973-2063
    DOI 10.6026/97320630014350
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  3. Article ; Online: Designing Self-Inhibitory fusion peptide analogous to viral spike protein against novel severe acute respiratory syndrome (SARS-CoV-2).

    Singh, Indra / Singh, Shalini / Ojha, Krishna Kumar / Yadav, Neetu Singh

    Journal of biomolecular structure & dynamics

    2021  Volume 40, Issue 21, Page(s) 11357–11372

    Abstract: COVID-19 is a highly contagious viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is declared pandemic by the World Health Organization (WHO). The spike protein of SARS-CoV-2 is a key component playing a ... ...

    Abstract COVID-19 is a highly contagious viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is declared pandemic by the World Health Organization (WHO). The spike protein of SARS-CoV-2 is a key component playing a pivotal role in facilitating viral fusion as well as release of genome into the host cell. Till date there is no clinically approved vaccine or drug available against Covid-19. We designed four hydrophobic inhibitory peptides (ITPs) based on WWIHS (Wimley and White interfacial hydrophobicity scale) score, targeting the HR1 domain of spike protein. Two inhibitory peptides out of four have a strong affinity to the hydrophobic surface of HR1 domain in pre-fusion spike protein. The MD simulation result showed the strong accommodation of ITPs with HR1 domain surface. These self-inhibitory peptides mimic the function of HR2 by binding to HR1 domain, thus inhibiting the formation of HR1-HR2 post-fusion complex, which is a key structure for virus-host tropism.Communicated by Ramaswamy H. Sarma.
    MeSH term(s) Amino Acid Sequence ; Peptides/pharmacology ; SARS-CoV-2/drug effects ; Spike Glycoprotein, Coronavirus/antagonists & inhibitors ; Viral Envelope Proteins/chemistry
    Chemical Substances Peptides ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Viral Envelope Proteins
    Language English
    Publishing date 2021-08-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2021.1960192
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 2093: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  4. Article ; Online: Molecular dynamics simulations and experimental studies reveal differential permeability of withaferin-A and withanone across the model cell membrane.

    Wadhwa, Renu / Yadav, Neetu Singh / Katiyar, Shashank P / Yaguchi, Tomoko / Lee, Chohee / Ahn, Hyomin / Yun, Chae-Ok / Kaul, Sunil C / Sundar, Durai

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 2352

    Abstract: Poor bioavailability due to the inability to cross the cell membrane is one of the major reasons for the failure of a drug in clinical trials. We have used molecular dynamics simulations to predict the membrane permeability of natural drugs-withanolides ( ...

    Abstract Poor bioavailability due to the inability to cross the cell membrane is one of the major reasons for the failure of a drug in clinical trials. We have used molecular dynamics simulations to predict the membrane permeability of natural drugs-withanolides (withaferin-A and withanone) that have similar structures but remarkably differ in their cytotoxicity. We found that whereas withaferin-A, could proficiently transverse through the model membrane, withanone showed weak permeability. The free energy profiles for the interaction of withanolides with the model bilayer membrane revealed that whereas the polar head group of the membrane caused high resistance for the passage of withanone, the interior of the membrane behaves similarly for both withanolides. The solvation analysis further revealed that the high solvation of terminal O5 oxygen of withaferin-A was the major driving force for its high permeability; it interacted with the phosphate group of the membrane that led to its smooth passage across the bilayer. The computational predictions were tested by raising and recruiting unique antibodies that react to withaferin-A and withanone. The time-lapsed analyses of control and treated cells demonstrated higher permeation of withaferin-A as compared to withanone. The concurrence between the computation and experimental results thus re-emphasised the use of computational methods for predicting permeability and hence bioavailability of natural drug compounds in the drug development process.
    MeSH term(s) Cell Membrane/metabolism ; Humans ; Models, Theoretical ; Molecular Dynamics Simulation ; Oxygen/metabolism ; Withanolides/chemistry
    Chemical Substances Withanolides ; withanone (GY036XA633) ; withaferin A (L6DO3QW4K5) ; Oxygen (S88TT14065)
    Language English
    Publishing date 2021-01-27
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-81729-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  5. Article ; Online: Finding potent inhibitors for COVID-19 main protease (M

    Motiwale, Mohit / Yadav, Neetu Singh / Kumar, Sushil / Kushwaha, Tushar / Choudhir, Gourav / Sharma, Supriya / Singour, Pradeep Kumar

    Journal of biomolecular structure & dynamics

    2020  Volume 40, Issue 4, Page(s) 1534–1545

    Abstract: SARS-CoV-2 is liable for the worldwide coronavirus disease (COVID-19) exigency. This pandemic created the need for all viable treatment strategies available in the market. In this scenario, computer-aided drug design techniques can be efficiently applied ...

    Abstract SARS-CoV-2 is liable for the worldwide coronavirus disease (COVID-19) exigency. This pandemic created the need for all viable treatment strategies available in the market. In this scenario, computer-aided drug design techniques can be efficiently applied for the quick identification of promising drug repurposing candidates. In the current study, we applied the molecular docking approach in conjugation with molecular dynamics (MD) simulations to find out potential inhibitors against M
    MeSH term(s) COVID-19 ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Peptide Hydrolases ; Protease Inhibitors/pharmacology ; SARS-CoV-2
    Chemical Substances Protease Inhibitors ; Peptide Hydrolases (EC 3.4.-)
    Keywords covid19
    Language English
    Publishing date 2020-10-08
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2020.1829501
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 2093: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  6. Article: Finding potent inhibitors for COVID-19 main protease (Mpro): an in silico approach using SARS-CoV-3CL protease inhibitors for combating CORONA

    Motiwale, Mohit / Yadav, Neetu Singh / Kumar, Sushil / Kushwaha, Tushar / Choudhir, Gourav / Sharma, Supriya / Singour, Pradeep Kumar

    J Biomol Struct Dyn

    Abstract: SARS-CoV-2 is liable for the worldwide coronavirus disease (COVID-19) exigency. This pandemic created the need for all viable treatment strategies available in the market. In this scenario, computer-aided drug design techniques can be efficiently applied ...

    Abstract SARS-CoV-2 is liable for the worldwide coronavirus disease (COVID-19) exigency. This pandemic created the need for all viable treatment strategies available in the market. In this scenario, computer-aided drug design techniques can be efficiently applied for the quick identification of promising drug repurposing candidates. In the current study, we applied the molecular docking approach in conjugation with molecular dynamics (MD) simulations to find out potential inhibitors against Mpro of SARS-CoV-2 from previously reported SARS-3CL protease inhibitors. Our results showed that N-substituted isatin derivatives and pyrazolone compounds could be used as a potent inhibitor and may possess an anti-viral activity against SARS-CoV-2. However, further experimental investigation and validation of the selected hits are required to find out their suitability for clinical trials. Communicated by Ramaswamy H. Sarma.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #837671
    Database COVID19

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  7. Article ; Online: Finding potent inhibitors for COVID-19 main protease (Mpro)

    Motiwale, Mohit / Yadav, Neetu Singh / Kumar, Sushil / Kushwaha, Tushar / Choudhir, Gourav / Sharma, Supriya / Singour, Pradeep Kumar

    Journal of Biomolecular Structure and Dynamics

    an in silico approach using SARS-CoV-3CL protease inhibitors for combating CORONA

    2020  , Page(s) 1–12

    Keywords Molecular Biology ; Structural Biology ; General Medicine ; covid19
    Language English
    Publisher Informa UK Limited
    Publishing country uk
    Document type Article ; Online
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2020.1829501
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 2093: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  8. Article ; Online: Role of Ser65, His148 and Thr203 in the Organic Solvent-dependent Spectral Shift in Green Fluorescent Protein.

    Kaur, Jasvir / Yadav, Neetu Singh / Singh, Moirangthem Kiran / Khan, Mohd Jahir / Sen, Sobhan / Dixit, Aparna / Choudhury, Devapriya

    Photochemistry and photobiology

    2018  Volume 95, Issue 2, Page(s) 543–555

    Abstract: The photophysics of green fluorescent protein (GFP) is remarkable because of its exceptional property of excited state proton transfer (ESPT) and the presence of a functional proton wire. Another interesting property of wild-type GFP is that its ... ...

    Abstract The photophysics of green fluorescent protein (GFP) is remarkable because of its exceptional property of excited state proton transfer (ESPT) and the presence of a functional proton wire. Another interesting property of wild-type GFP is that its absorption and fluorescence excitation spectra are sensitive to the presence of polar organic solvents even at very low concentrations. Here, we use a combination of methodologies including site-specific mutagenesis, absorption spectroscopy, steady-state and time-resolved fluorescence measurements and all-atom molecular dynamics simulations in explicit solvent, to uncover the mechanism behind the unique spectral sensitivity of GFP toward organic solvents. Based on the evidences provided herein, we suggest that organic solvent-induced changes in the proton wire prevent ground state movement of a proton through the wire and thus bring about the spectral changes observed. The present study can not only help to understand the mechanism of proton transfer by further dissecting the intricate steps in GFP photophysics but also encourages to develop GFP-based organic solvent biosensors.
    MeSH term(s) Green Fluorescent Proteins/chemistry ; Histidine/chemistry ; Organic Chemicals/chemistry ; Serine/chemistry ; Solvents/chemistry ; Threonine/chemistry
    Chemical Substances Organic Chemicals ; Solvents ; Green Fluorescent Proteins (147336-22-9) ; Threonine (2ZD004190S) ; Serine (452VLY9402) ; Histidine (4QD397987E)
    Language English
    Publishing date 2018-10-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 123540-0
    ISSN 1751-1097 ; 0031-8655
    ISSN (online) 1751-1097
    ISSN 0031-8655
    DOI 10.1111/php.13018
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.B 1686: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

To top